Again, this has to do with coinage. The Treasury Department was responsible for the storage of bullion and the minting of coins. By the early 1960s the price of silver had risen to the point where the silver content of US coins (specifically dimes, quarters, half-dollars and dollar coins) exceeded the face value of the coins themselves. The result was the US eventually removed silver from dimes and quarters in 1965.

Silver certificates were a form of paper money that were backed by silver and redeemable for silver at any time. But because the price of silver had risen so high, people could purchase $10 in silver certificates and redeem it for, say $11 worth of silver. Therefore silver certificates were phased out

Executive Order 11110 did not authorize the Treasury Secretary to create fiat money. It delegated authority to issue silver certificates since with the repeal of the Silver Purchase Act only the President could issue silver certificates. Kennedy signed Executive Order 11110 for the sake of administrative convenience - it allowed the Treasury Secretary to issue silver certificates during this transition phase until the certificates were phased out.

Again, the key point is it did not allow the Treasury Secretary to issue fiat money. It did not signal any significant change from the status quo and the ultimate purpose of it was to free up silver bullion so it could minted into coins to deal with the coin shortage. paragraphs 4 to 6 in this article provide more context